Starting phenix.real_space_refine (version: dev) on Sat Apr 9 00:49:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ray_4787/04_2022/6ray_4787_updated.pdb" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "3 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 75": "NH1" <-> "NH2" Residue "3 ASP 94": "OD1" <-> "OD2" Residue "3 ARG 106": "NH1" <-> "NH2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 158": "OD1" <-> "OD2" Residue "3 ASP 177": "OD1" <-> "OD2" Residue "3 GLU 203": "OE1" <-> "OE2" Residue "3 ASP 224": "OD1" <-> "OD2" Residue "3 ARG 225": "NH1" <-> "NH2" Residue "3 ARG 231": "NH1" <-> "NH2" Residue "3 ARG 239": "NH1" <-> "NH2" Residue "3 ARG 245": "NH1" <-> "NH2" Residue "3 ARG 254": "NH1" <-> "NH2" Residue "3 GLU 268": "OE1" <-> "OE2" Residue "3 ARG 275": "NH1" <-> "NH2" Residue "3 GLU 292": "OE1" <-> "OE2" Residue "3 ARG 329": "NH1" <-> "NH2" Residue "3 ASP 333": "OD1" <-> "OD2" Residue "3 ARG 351": "NH1" <-> "NH2" Residue "3 TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 359": "NH1" <-> "NH2" Residue "3 ARG 366": "NH1" <-> "NH2" Residue "3 ARG 387": "NH1" <-> "NH2" Residue "3 ARG 414": "NH1" <-> "NH2" Residue "3 GLU 422": "OE1" <-> "OE2" Residue "3 ARG 425": "NH1" <-> "NH2" Residue "3 TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 453": "NH1" <-> "NH2" Residue "3 ASP 455": "OD1" <-> "OD2" Residue "3 ASP 475": "OD1" <-> "OD2" Residue "3 ASP 494": "OD1" <-> "OD2" Residue "3 ARG 501": "NH1" <-> "NH2" Residue "3 ARG 503": "NH1" <-> "NH2" Residue "3 ARG 550": "NH1" <-> "NH2" Residue "3 ARG 552": "NH1" <-> "NH2" Residue "3 ARG 563": "NH1" <-> "NH2" Residue "3 GLU 587": "OE1" <-> "OE2" Residue "3 ARG 590": "NH1" <-> "NH2" Residue "3 ARG 603": "NH1" <-> "NH2" Residue "3 ARG 610": "NH1" <-> "NH2" Residue "3 ARG 624": "NH1" <-> "NH2" Residue "3 GLU 641": "OE1" <-> "OE2" Residue "4 ARG 174": "NH1" <-> "NH2" Residue "4 ASP 190": "OD1" <-> "OD2" Residue "4 GLU 208": "OE1" <-> "OE2" Residue "4 ASP 224": "OD1" <-> "OD2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 ARG 251": "NH1" <-> "NH2" Residue "4 TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 283": "OD1" <-> "OD2" Residue "4 ARG 303": "NH1" <-> "NH2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 341": "NH1" <-> "NH2" Residue "4 ARG 346": "NH1" <-> "NH2" Residue "4 GLU 348": "OE1" <-> "OE2" Residue "4 ASP 380": "OD1" <-> "OD2" Residue "4 ASP 389": "OD1" <-> "OD2" Residue "4 ARG 390": "NH1" <-> "NH2" Residue "4 TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 425": "NH1" <-> "NH2" Residue "4 ASP 428": "OD1" <-> "OD2" Residue "4 GLU 436": "OE1" <-> "OE2" Residue "4 ARG 447": "NH1" <-> "NH2" Residue "4 ARG 463": "NH1" <-> "NH2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 503": "NH1" <-> "NH2" Residue "4 ARG 531": "NH1" <-> "NH2" Residue "4 TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 554": "OE1" <-> "OE2" Residue "4 GLU 577": "OE1" <-> "OE2" Residue "4 ASP 583": "OD1" <-> "OD2" Residue "4 GLU 623": "OE1" <-> "OE2" Residue "4 ARG 629": "NH1" <-> "NH2" Residue "4 VAL 652": "CG1" <-> "CG2" Residue "4 GLU 658": "OE1" <-> "OE2" Residue "4 ARG 663": "NH1" <-> "NH2" Residue "4 TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 676": "NH1" <-> "NH2" Residue "4 ASP 681": "OD1" <-> "OD2" Residue "4 ARG 690": "NH1" <-> "NH2" Residue "4 ARG 697": "NH1" <-> "NH2" Residue "4 ARG 711": "NH1" <-> "NH2" Residue "4 ASP 718": "OD1" <-> "OD2" Residue "4 ARG 726": "NH1" <-> "NH2" Residue "4 ARG 734": "NH1" <-> "NH2" Residue "4 GLU 737": "OE1" <-> "OE2" Residue "4 ARG 750": "NH1" <-> "NH2" Residue "4 ARG 765": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 4": "NH1" <-> "NH2" Residue "7 ARG 10": "NH1" <-> "NH2" Residue "7 ASP 26": "OD1" <-> "OD2" Residue "7 ASP 53": "OD1" <-> "OD2" Residue "7 ARG 71": "NH1" <-> "NH2" Residue "7 ASP 121": "OD1" <-> "OD2" Residue "7 ARG 123": "NH1" <-> "NH2" Residue "7 ARG 133": "NH1" <-> "NH2" Residue "7 ASP 205": "OD1" <-> "OD2" Residue "7 ARG 212": "NH1" <-> "NH2" Residue "7 ARG 219": "NH1" <-> "NH2" Residue "7 TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 234": "OE1" <-> "OE2" Residue "7 ARG 258": "NH1" <-> "NH2" Residue "7 PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 302": "NH1" <-> "NH2" Residue "7 ASP 310": "OD1" <-> "OD2" Residue "7 ASP 330": "OD1" <-> "OD2" Residue "7 GLU 343": "OE1" <-> "OE2" Residue "7 ASP 349": "OD1" <-> "OD2" Residue "7 ARG 365": "NH1" <-> "NH2" Residue "7 ARG 372": "NH1" <-> "NH2" Residue "7 ASP 382": "OD1" <-> "OD2" Residue "7 ARG 396": "NH1" <-> "NH2" Residue "7 ARG 407": "NH1" <-> "NH2" Residue "7 ARG 455": "NH1" <-> "NH2" Residue "7 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 494": "NH1" <-> "NH2" Residue "7 ARG 498": "NH1" <-> "NH2" Residue "7 ARG 499": "NH1" <-> "NH2" Residue "7 ARG 527": "NH1" <-> "NH2" Residue "7 ARG 532": "NH1" <-> "NH2" Residue "7 ARG 550": "NH1" <-> "NH2" Residue "7 ARG 561": "NH1" <-> "NH2" Residue "7 TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 568": "NH1" <-> "NH2" Residue "7 ARG 590": "NH1" <-> "NH2" Residue "7 ARG 593": "NH1" <-> "NH2" Residue "7 ARG 620": "NH1" <-> "NH2" Residue "7 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "6 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 95": "NH1" <-> "NH2" Residue "6 ARG 114": "NH1" <-> "NH2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 ARG 160": "NH1" <-> "NH2" Residue "6 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 175": "NH1" <-> "NH2" Residue "6 ARG 182": "NH1" <-> "NH2" Residue "6 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 201": "NH1" <-> "NH2" Residue "6 GLU 208": "OE1" <-> "OE2" Residue "6 ARG 211": "NH1" <-> "NH2" Residue "6 ARG 216": "NH1" <-> "NH2" Residue "6 GLU 219": "OE1" <-> "OE2" Residue "6 ARG 223": "NH1" <-> "NH2" Residue "6 ARG 257": "NH1" <-> "NH2" Residue "6 ARG 263": "NH1" <-> "NH2" Residue "6 ARG 282": "NH1" <-> "NH2" Residue "6 ARG 287": "NH1" <-> "NH2" Residue "6 ARG 301": "NH1" <-> "NH2" Residue "6 ASP 316": "OD1" <-> "OD2" Residue "6 ARG 336": "NH1" <-> "NH2" Residue "6 ARG 358": "NH1" <-> "NH2" Residue "6 ARG 379": "NH1" <-> "NH2" Residue "6 PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 407": "NH1" <-> "NH2" Residue "6 ARG 427": "NH1" <-> "NH2" Residue "6 GLU 430": "OE1" <-> "OE2" Residue "6 ASP 433": "OD1" <-> "OD2" Residue "6 GLU 437": "OE1" <-> "OE2" Residue "6 ARG 460": "NH1" <-> "NH2" Residue "6 ASP 503": "OD1" <-> "OD2" Residue "6 ARG 504": "NH1" <-> "NH2" Residue "6 ARG 521": "NH1" <-> "NH2" Residue "6 ASP 523": "OD1" <-> "OD2" Residue "6 ASP 530": "OD1" <-> "OD2" Residue "6 ARG 542": "NH1" <-> "NH2" Residue "6 ASP 546": "OD1" <-> "OD2" Residue "6 GLU 556": "OE1" <-> "OE2" Residue "6 ARG 557": "NH1" <-> "NH2" Residue "6 ARG 561": "NH1" <-> "NH2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 596": "NH1" <-> "NH2" Residue "6 ARG 603": "NH1" <-> "NH2" Residue "6 ARG 631": "NH1" <-> "NH2" Residue "6 ARG 635": "NH1" <-> "NH2" Residue "6 ARG 642": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 62": "NH1" <-> "NH2" Residue "5 GLU 68": "OE1" <-> "OE2" Residue "5 ASP 71": "OD1" <-> "OD2" Residue "5 GLU 77": "OE1" <-> "OE2" Residue "5 ARG 99": "NH1" <-> "NH2" Residue "5 GLU 113": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 199": "NH1" <-> "NH2" Residue "5 GLU 235": "OE1" <-> "OE2" Residue "5 ASP 245": "OD1" <-> "OD2" Residue "5 ARG 251": "NH1" <-> "NH2" Residue "5 ARG 267": "NH1" <-> "NH2" Residue "5 GLU 279": "OE1" <-> "OE2" Residue "5 TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 291": "NH1" <-> "NH2" Residue "5 ARG 307": "NH1" <-> "NH2" Residue "5 ASP 314": "OD1" <-> "OD2" Residue "5 ARG 320": "NH1" <-> "NH2" Residue "5 ARG 321": "NH1" <-> "NH2" Residue "5 GLU 330": "OE1" <-> "OE2" Residue "5 ARG 331": "NH1" <-> "NH2" Residue "5 ARG 344": "NH1" <-> "NH2" Residue "5 ARG 359": "NH1" <-> "NH2" Residue "5 ARG 361": "NH1" <-> "NH2" Residue "5 ARG 368": "NH1" <-> "NH2" Residue "5 ASP 379": "OD1" <-> "OD2" Residue "5 TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 422": "NH1" <-> "NH2" Residue "5 GLU 427": "OE1" <-> "OE2" Residue "5 ASP 435": "OD1" <-> "OD2" Residue "5 GLU 443": "OE1" <-> "OE2" Residue "5 ASP 493": "OD1" <-> "OD2" Residue "5 GLU 499": "OE1" <-> "OE2" Residue "5 ASP 522": "OD1" <-> "OD2" Residue "5 GLU 523": "OE1" <-> "OE2" Residue "5 GLU 552": "OE1" <-> "OE2" Residue "5 GLU 575": "OE1" <-> "OE2" Residue "5 ARG 610": "NH1" <-> "NH2" Residue "5 ARG 626": "NH1" <-> "NH2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 170": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L GLU 72": "OE1" <-> "OE2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "M GLU 93": "OE1" <-> "OE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N ASP 28": "OD1" <-> "OD2" Residue "N GLU 40": "OE1" <-> "OE2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 197": "OD1" <-> "OD2" Residue "2 ARG 177": "NH1" <-> "NH2" Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 ARG 189": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 201": "NH1" <-> "NH2" Residue "2 ARG 206": "NH1" <-> "NH2" Residue "2 GLU 277": "OE1" <-> "OE2" Residue "2 ARG 292": "NH1" <-> "NH2" Residue "2 GLU 331": "OE1" <-> "OE2" Residue "2 ARG 356": "NH1" <-> "NH2" Residue "2 GLU 365": "OE1" <-> "OE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ASP 380": "OD1" <-> "OD2" Residue "2 GLU 396": "OE1" <-> "OE2" Residue "2 ASP 408": "OD1" <-> "OD2" Residue "2 ASP 414": "OD1" <-> "OD2" Residue "2 ASP 443": "OD1" <-> "OD2" Residue "2 ASP 455": "OD1" <-> "OD2" Residue "2 ARG 457": "NH1" <-> "NH2" Residue "2 ARG 461": "NH1" <-> "NH2" Residue "2 ARG 478": "NH1" <-> "NH2" Residue "2 ARG 499": "NH1" <-> "NH2" Residue "2 ASP 575": "OD1" <-> "OD2" Residue "2 ASP 579": "OD1" <-> "OD2" Residue "2 ARG 621": "NH1" <-> "NH2" Residue "2 GLU 636": "OE1" <-> "OE2" Residue "2 ASP 657": "OD1" <-> "OD2" Residue "2 ARG 698": "NH1" <-> "NH2" Residue "2 TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 709": "NH1" <-> "NH2" Residue "2 ASP 718": "OD1" <-> "OD2" Residue "2 ARG 728": "NH1" <-> "NH2" Residue "2 ARG 742": "NH1" <-> "NH2" Residue "2 ARG 756": "NH1" <-> "NH2" Residue "2 ARG 760": "NH1" <-> "NH2" Residue "2 ARG 773": "NH1" <-> "NH2" Residue "2 GLU 777": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 39071 Number of models: 1 Model: "" Number of chains: 18 Chain: "3" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4685 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "4" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4901 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "7" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4577 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 562} Unresolved chain links: 1 Chain breaks: 11 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "6" Number of atoms: 4748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4748 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 580} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "5" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4505 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 25, 'TRANS': 551} Chain breaks: 10 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4555 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 552} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1504 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1377 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1627 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ILE%COO:oxt': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "2" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4731 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 571} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.44, per 1000 atoms: 0.55 Number of scatterers: 39071 At special positions: 0 Unit cell: (204.12, 189, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 208 16.00 P 29 15.00 O 7479 8.00 N 6871 7.00 C 24484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.55 Conformation dependent library (CDL) restraints added in 5.6 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 28 sheets defined 31.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain '3' and resid 7 through 19 removed outlier: 3.589A pdb=" N ASP 3 18 " --> pdb=" O GLU 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 28 Processing helix chain '3' and resid 48 through 54 Processing helix chain '3' and resid 56 through 64 removed outlier: 4.212A pdb=" N LEU 3 62 " --> pdb=" O ARG 3 58 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 84 Processing helix chain '3' and resid 87 through 89 No H-bonds generated for 'chain '3' and resid 87 through 89' Processing helix chain '3' and resid 202 through 204 No H-bonds generated for 'chain '3' and resid 202 through 204' Processing helix chain '3' and resid 275 through 283 Processing helix chain '3' and resid 288 through 295 removed outlier: 4.338A pdb=" N PHE 3 291 " --> pdb=" O ASN 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 309 through 316 removed outlier: 4.749A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 354 Processing helix chain '3' and resid 411 through 423 removed outlier: 4.006A pdb=" N THR 3 415 " --> pdb=" O ASP 3 411 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA 3 416 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 502 removed outlier: 3.938A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 559 through 567 removed outlier: 4.393A pdb=" N TYR 3 565 " --> pdb=" O PHE 3 561 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE 3 566 " --> pdb=" O MET 3 562 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS 3 567 " --> pdb=" O ARG 3 563 " (cutoff:3.500A) Processing helix chain '3' and resid 569 through 571 No H-bonds generated for 'chain '3' and resid 569 through 571' Processing helix chain '3' and resid 580 through 594 Processing helix chain '3' and resid 601 through 603 No H-bonds generated for 'chain '3' and resid 601 through 603' Processing helix chain '3' and resid 609 through 623 removed outlier: 3.764A pdb=" N GLU 3 613 " --> pdb=" O ARG 3 610 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU 3 615 " --> pdb=" O LEU 3 612 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU 3 618 " --> pdb=" O LEU 3 615 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR 3 620 " --> pdb=" O ARG 3 617 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS 3 622 " --> pdb=" O SER 3 619 " (cutoff:3.500A) Processing helix chain '3' and resid 633 through 639 Processing helix chain '3' and resid 641 through 647 removed outlier: 3.908A pdb=" N TYR 3 647 " --> pdb=" O VAL 3 643 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 173 Processing helix chain '4' and resid 178 through 181 No H-bonds generated for 'chain '4' and resid 178 through 181' Processing helix chain '4' and resid 195 through 204 Processing helix chain '4' and resid 216 through 219 removed outlier: 3.674A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 216 through 219' Processing helix chain '4' and resid 224 through 231 Processing helix chain '4' and resid 237 through 251 removed outlier: 4.679A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU 4 250 " --> pdb=" O GLU 4 246 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG 4 251 " --> pdb=" O MET 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 446 through 456 removed outlier: 4.488A pdb=" N ALA 4 455 " --> pdb=" O GLN 4 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS 4 456 " --> pdb=" O LEU 4 453 " (cutoff:3.500A) Processing helix chain '4' and resid 458 through 468 removed outlier: 3.853A pdb=" N TYR 4 461 " --> pdb=" O PRO 4 458 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU 4 464 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE 4 468 " --> pdb=" O ALA 4 465 " (cutoff:3.500A) Processing helix chain '4' and resid 476 through 486 removed outlier: 3.990A pdb=" N LYS 4 480 " --> pdb=" O ASP 4 477 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU 4 484 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 4 486 " --> pdb=" O LEU 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 528 removed outlier: 3.651A pdb=" N LEU 4 522 " --> pdb=" O LYS 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 578 through 580 No H-bonds generated for 'chain '4' and resid 578 through 580' Processing helix chain '4' and resid 632 through 635 No H-bonds generated for 'chain '4' and resid 632 through 635' Processing helix chain '4' and resid 659 through 669 removed outlier: 4.171A pdb=" N ARG 4 663 " --> pdb=" O ILE 4 659 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) Processing helix chain '4' and resid 671 through 674 No H-bonds generated for 'chain '4' and resid 671 through 674' Processing helix chain '4' and resid 690 through 697 Processing helix chain '4' and resid 710 through 723 removed outlier: 3.845A pdb=" N GLN 4 714 " --> pdb=" O GLN 4 710 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL 4 722 " --> pdb=" O ASP 4 718 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY 4 723 " --> pdb=" O MET 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 735 through 748 removed outlier: 3.680A pdb=" N ALA 4 745 " --> pdb=" O ARG 4 741 " (cutoff:3.500A) Processing helix chain '4' and resid 758 through 767 Processing helix chain '7' and resid 8 through 18 Processing helix chain '7' and resid 32 through 40 Processing helix chain '7' and resid 52 through 58 removed outlier: 4.194A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 72 through 83 removed outlier: 3.668A pdb=" N ILE 7 81 " --> pdb=" O PHE 7 77 " (cutoff:3.500A) Processing helix chain '7' and resid 99 through 106 removed outlier: 3.934A pdb=" N GLU 7 104 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 226 No H-bonds generated for 'chain '7' and resid 224 through 226' Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 322 through 329 removed outlier: 4.584A pdb=" N GLU 7 325 " --> pdb=" O GLU 7 322 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA 7 328 " --> pdb=" O GLU 7 325 " (cutoff:3.500A) Processing helix chain '7' and resid 335 through 339 Processing helix chain '7' and resid 348 through 359 Processing helix chain '7' and resid 366 through 368 No H-bonds generated for 'chain '7' and resid 366 through 368' Processing helix chain '7' and resid 387 through 397 removed outlier: 4.100A pdb=" N LEU 7 391 " --> pdb=" O LYS 7 387 " (cutoff:3.500A) Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 453 through 462 removed outlier: 3.756A pdb=" N THR 7 456 " --> pdb=" O GLN 7 453 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU 7 460 " --> pdb=" O ALA 7 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 7 461 " --> pdb=" O ILE 7 458 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 513 Processing helix chain '7' and resid 529 through 542 removed outlier: 3.535A pdb=" N ILE 7 537 " --> pdb=" O LEU 7 533 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 556 through 565 removed outlier: 3.692A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 591 removed outlier: 4.261A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 7 581 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR 7 585 " --> pdb=" O VAL 7 582 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 591 " --> pdb=" O LEU 7 588 " (cutoff:3.500A) Processing helix chain '7' and resid 603 through 620 removed outlier: 4.512A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 7 609 " --> pdb=" O ASN 7 605 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 627 through 640 removed outlier: 3.520A pdb=" N GLU 7 632 " --> pdb=" O ASP 7 628 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 29 removed outlier: 3.578A pdb=" N LEU 6 24 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP 6 27 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE 6 28 " --> pdb=" O PHE 6 25 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 48 removed outlier: 3.764A pdb=" N GLU 6 48 " --> pdb=" O ALA 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 64 Processing helix chain '6' and resid 70 through 73 No H-bonds generated for 'chain '6' and resid 70 through 73' Processing helix chain '6' and resid 77 through 94 Proline residue: 6 82 - end of helix Processing helix chain '6' and resid 122 through 124 No H-bonds generated for 'chain '6' and resid 122 through 124' Processing helix chain '6' and resid 224 through 226 No H-bonds generated for 'chain '6' and resid 224 through 226' Processing helix chain '6' and resid 324 through 332 removed outlier: 4.607A pdb=" N HIS 6 327 " --> pdb=" O ALA 6 324 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR 6 330 " --> pdb=" O HIS 6 327 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU 6 331 " --> pdb=" O LYS 6 328 " (cutoff:3.500A) Processing helix chain '6' and resid 337 through 344 Processing helix chain '6' and resid 356 through 359 No H-bonds generated for 'chain '6' and resid 356 through 359' Processing helix chain '6' and resid 361 through 364 Processing helix chain '6' and resid 398 through 404 removed outlier: 3.550A pdb=" N SER 6 402 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) Processing helix chain '6' and resid 461 through 468 removed outlier: 4.193A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 508 through 512 Processing helix chain '6' and resid 517 through 521 removed outlier: 3.935A pdb=" N ARG 6 521 " --> pdb=" O ILE 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 534 through 544 removed outlier: 3.613A pdb=" N ILE 6 540 " --> pdb=" O VAL 6 536 " (cutoff:3.500A) Processing helix chain '6' and resid 561 through 572 removed outlier: 4.409A pdb=" N THR 6 569 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 6 570 " --> pdb=" O ARG 6 566 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG 6 572 " --> pdb=" O VAL 6 568 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 597 removed outlier: 4.503A pdb=" N VAL 6 587 " --> pdb=" O GLY 6 583 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLU 6 588 " --> pdb=" O HIS 6 584 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG 6 596 " --> pdb=" O HIS 6 592 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 626 Processing helix chain '6' and resid 634 through 651 removed outlier: 3.642A pdb=" N LEU 6 643 " --> pdb=" O ALA 6 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 6 644 " --> pdb=" O PHE 6 641 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE 6 648 " --> pdb=" O ASN 6 645 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 31 No H-bonds generated for 'chain '5' and resid 28 through 31' Processing helix chain '5' and resid 33 through 40 Processing helix chain '5' and resid 53 through 57 Processing helix chain '5' and resid 72 through 75 No H-bonds generated for 'chain '5' and resid 72 through 75' Processing helix chain '5' and resid 80 through 83 No H-bonds generated for 'chain '5' and resid 80 through 83' Processing helix chain '5' and resid 87 through 105 removed outlier: 4.069A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP 5 103 " --> pdb=" O ARG 5 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 137 through 139 No H-bonds generated for 'chain '5' and resid 137 through 139' Processing helix chain '5' and resid 211 through 213 No H-bonds generated for 'chain '5' and resid 211 through 213' Processing helix chain '5' and resid 313 through 323 removed outlier: 3.612A pdb=" N MET 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 334 removed outlier: 4.007A pdb=" N GLN 5 334 " --> pdb=" O ARG 5 331 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 331 through 334' Processing helix chain '5' and resid 344 through 350 removed outlier: 3.875A pdb=" N ALA 5 349 " --> pdb=" O ASP 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 384 through 389 removed outlier: 3.583A pdb=" N LEU 5 388 " --> pdb=" O LYS 5 384 " (cutoff:3.500A) Processing helix chain '5' and resid 420 through 422 No H-bonds generated for 'chain '5' and resid 420 through 422' Processing helix chain '5' and resid 453 through 459 removed outlier: 4.572A pdb=" N ALA 5 458 " --> pdb=" O ALA 5 454 " (cutoff:3.500A) Processing helix chain '5' and resid 490 through 494 Processing helix chain '5' and resid 506 through 508 No H-bonds generated for 'chain '5' and resid 506 through 508' Processing helix chain '5' and resid 523 through 531 removed outlier: 3.671A pdb=" N ILE 5 527 " --> pdb=" O GLU 5 523 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR 5 528 " --> pdb=" O SER 5 524 " (cutoff:3.500A) Processing helix chain '5' and resid 534 through 537 No H-bonds generated for 'chain '5' and resid 534 through 537' Processing helix chain '5' and resid 555 through 567 removed outlier: 5.551A pdb=" N THR 5 567 " --> pdb=" O HIS 5 563 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 625 removed outlier: 7.034A pdb=" N VAL 5 615 " --> pdb=" O ARG 5 610 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE 5 616 " --> pdb=" O GLN 5 611 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG 5 617 " --> pdb=" O LEU 5 612 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE 5 618 " --> pdb=" O GLU 5 613 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA 5 623 " --> pdb=" O SER 5 619 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) Processing helix chain '5' and resid 638 through 650 removed outlier: 4.253A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 5 648 " --> pdb=" O GLN 5 644 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP 5 649 " --> pdb=" O VAL 5 645 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 5 650 " --> pdb=" O SER 5 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 28 through 42 removed outlier: 4.206A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 removed outlier: 3.972A pdb=" N LYS A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 106 through 109 No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.824A pdb=" N LEU A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 186 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 195 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 196 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.877A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.741A pdb=" N TRP A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 265 removed outlier: 5.287A pdb=" N GLU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.341A pdb=" N ARG A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.019A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.238A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 347 through 360 removed outlier: 4.751A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.717A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 395 " --> pdb=" O TYR A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 390 through 395' Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.702A pdb=" N SER A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 4.006A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A 440 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 447 No H-bonds generated for 'chain 'A' and resid 444 through 447' Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.928A pdb=" N LEU A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 541 removed outlier: 3.934A pdb=" N ALA A 538 " --> pdb=" O PHE A 535 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 540 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 541 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'H' and resid 11 through 17 removed outlier: 3.959A pdb=" N LEU H 16 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS H 17 " --> pdb=" O ASP H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 45 through 48 No H-bonds generated for 'chain 'H' and resid 45 through 48' Processing helix chain 'H' and resid 61 through 98 Proline residue: H 65 - end of helix removed outlier: 3.827A pdb=" N ASN H 68 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA H 72 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H 73 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG H 76 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS H 78 " --> pdb=" O GLN H 75 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 79 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS H 80 " --> pdb=" O ASN H 77 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 82 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR H 84 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU H 87 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG H 90 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG H 91 " --> pdb=" O ARG H 88 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE H 92 " --> pdb=" O CYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 125 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'L' and resid 10 through 12 No H-bonds generated for 'chain 'L' and resid 10 through 12' Processing helix chain 'L' and resid 50 through 53 No H-bonds generated for 'chain 'L' and resid 50 through 53' Processing helix chain 'L' and resid 74 through 80 removed outlier: 5.397A pdb=" N LYS L 79 " --> pdb=" O LYS L 75 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 105 Proline residue: L 104 - end of helix Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.667A pdb=" N LYS L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 134 Processing helix chain 'L' and resid 153 through 157 Processing helix chain 'L' and resid 161 through 168 removed outlier: 3.852A pdb=" N ASP L 165 " --> pdb=" O PRO L 161 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 removed outlier: 3.852A pdb=" N THR L 175 " --> pdb=" O ARG L 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 172 through 175' Processing helix chain 'M' and resid 56 through 59 Processing helix chain 'M' and resid 79 through 85 removed outlier: 4.624A pdb=" N VAL M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 111 removed outlier: 4.328A pdb=" N THR M 109 " --> pdb=" O GLY M 105 " (cutoff:3.500A) Proline residue: M 110 - end of helix Processing helix chain 'M' and resid 118 through 130 removed outlier: 3.945A pdb=" N PHE M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU M 125 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG M 128 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL M 129 " --> pdb=" O LEU M 125 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG M 130 " --> pdb=" O ARG M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 171 removed outlier: 3.974A pdb=" N ASN M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 171 " --> pdb=" O TYR M 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 50 removed outlier: 5.664A pdb=" N THR N 44 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 45 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 78 removed outlier: 5.690A pdb=" N MET N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL N 67 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN N 69 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL N 70 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS N 72 " --> pdb=" O GLN N 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU N 75 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 96 removed outlier: 3.529A pdb=" N HIS N 90 " --> pdb=" O ARG N 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 114 removed outlier: 3.911A pdb=" N SER N 103 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU N 105 " --> pdb=" O MET N 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 108 " --> pdb=" O TYR N 104 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN N 110 " --> pdb=" O ARG N 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE N 112 " --> pdb=" O ARG N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 135 through 154 removed outlier: 3.864A pdb=" N PHE N 140 " --> pdb=" O GLU N 137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN N 142 " --> pdb=" O LYS N 139 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA N 145 " --> pdb=" O GLN N 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN N 147 " --> pdb=" O PHE N 144 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU N 150 " --> pdb=" O ASN N 147 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TYR N 151 " --> pdb=" O VAL N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 222 No H-bonds generated for 'chain 'N' and resid 219 through 222' Processing helix chain '2' and resid 176 through 185 removed outlier: 4.168A pdb=" N ALA 2 181 " --> pdb=" O THR 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 199 through 210 removed outlier: 3.720A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 225 Processing helix chain '2' and resid 237 through 255 removed outlier: 3.528A pdb=" N LEU 2 241 " --> pdb=" O PRO 2 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE 2 255 " --> pdb=" O MET 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 447 through 450 No H-bonds generated for 'chain '2' and resid 447 through 450' Processing helix chain '2' and resid 456 through 464 removed outlier: 3.611A pdb=" N VAL 2 459 " --> pdb=" O PRO 2 456 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG 2 461 " --> pdb=" O ILE 2 458 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL 2 462 " --> pdb=" O VAL 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 474 through 485 removed outlier: 4.256A pdb=" N LEU 2 482 " --> pdb=" O ARG 2 478 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA 2 483 " --> pdb=" O ALA 2 479 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU 2 484 " --> pdb=" O LEU 2 480 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N PHE 2 485 " --> pdb=" O ALA 2 481 " (cutoff:3.500A) Processing helix chain '2' and resid 520 through 524 Processing helix chain '2' and resid 579 through 590 removed outlier: 3.886A pdb=" N SER 2 584 " --> pdb=" O GLN 2 580 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 2 585 " --> pdb=" O ASP 2 581 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 641 removed outlier: 4.057A pdb=" N SER 2 640 " --> pdb=" O GLU 2 636 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ARG 2 641 " --> pdb=" O PRO 2 637 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 636 through 641' Processing helix chain '2' and resid 654 through 669 Processing helix chain '2' and resid 697 through 707 removed outlier: 4.692A pdb=" N ALA 2 704 " --> pdb=" O ILE 2 701 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS 2 705 " --> pdb=" O VAL 2 702 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN 2 707 " --> pdb=" O ALA 2 704 " (cutoff:3.500A) Processing helix chain '2' and resid 717 through 729 removed outlier: 5.385A pdb=" N GLN 2 726 " --> pdb=" O MET 2 723 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU 2 727 " --> pdb=" O TYR 2 724 " (cutoff:3.500A) Processing helix chain '2' and resid 742 through 756 removed outlier: 4.328A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 752 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA 2 753 " --> pdb=" O ARG 2 749 " (cutoff:3.500A) Processing helix chain '2' and resid 765 through 782 removed outlier: 3.696A pdb=" N MET 2 774 " --> pdb=" O MET 2 770 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE 2 780 " --> pdb=" O LEU 2 776 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU 2 781 " --> pdb=" O GLU 2 777 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA 2 782 " --> pdb=" O SER 2 778 " (cutoff:3.500A) Processing helix chain '2' and resid 789 through 794 Processing sheet with id= A, first strand: chain '3' and resid 107 through 109 removed outlier: 6.336A pdb=" N CYS 3 123 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE 3 234 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY 3 126 " --> pdb=" O VAL 3 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 127 through 129 removed outlier: 3.942A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 135 through 138 Processing sheet with id= D, first strand: chain '3' and resid 140 through 143 Processing sheet with id= E, first strand: chain '3' and resid 237 through 239 removed outlier: 3.913A pdb=" N VAL 3 256 " --> pdb=" O ARG 3 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 426 through 428 removed outlier: 3.820A pdb=" N VAL 3 426 " --> pdb=" O LEU 3 437 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 3 437 " --> pdb=" O VAL 3 426 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 285 through 291 removed outlier: 3.602A pdb=" N GLY 4 290 " --> pdb=" O VAL 4 391 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 304 through 306 Processing sheet with id= I, first strand: chain '4' and resid 354 through 358 Processing sheet with id= J, first strand: chain '4' and resid 397 through 400 Processing sheet with id= K, first strand: chain '7' and resid 232 through 235 removed outlier: 3.743A pdb=" N CYS 7 257 " --> pdb=" O GLN 7 233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL 7 235 " --> pdb=" O ILE 7 255 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '7' and resid 376 through 380 removed outlier: 5.902A pdb=" N ILE 7 484 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU 7 379 " --> pdb=" O ILE 7 484 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA 7 486 " --> pdb=" O LEU 7 379 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN 7 402 " --> pdb=" O VAL 7 441 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS 7 443 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '7' and resid 176 through 179 removed outlier: 7.399A pdb=" N LYS 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 56 through 58 removed outlier: 6.319A pdb=" N ALA 6 107 " --> pdb=" O VAL 6 57 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '6' and resid 198 through 202 removed outlier: 3.548A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '6' and resid 408 through 412 removed outlier: 7.388A pdb=" N ILE 6 448 " --> pdb=" O ILE 6 409 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR 6 411 " --> pdb=" O ILE 6 448 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS 6 450 " --> pdb=" O THR 6 411 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '5' and resid 223 through 225 removed outlier: 3.559A pdb=" N LEU 5 224 " --> pdb=" O LEU 5 240 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 5 240 " --> pdb=" O LEU 5 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '5' and resid 374 through 378 removed outlier: 5.785A pdb=" N MET 5 513 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU 5 377 " --> pdb=" O MET 5 513 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE 5 515 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '5' and resid 439 through 442 Processing sheet with id= T, first strand: chain 'A' and resid 71 through 74 removed outlier: 6.575A pdb=" N THR A 94 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 74 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE A 96 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'A' and resid 284 through 289 removed outlier: 4.039A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 501 through 505 Processing sheet with id= W, first strand: chain 'L' and resid 14 through 18 Processing sheet with id= X, first strand: chain '2' and resid 215 through 218 Processing sheet with id= Y, first strand: chain '2' and resid 303 through 305 Processing sheet with id= Z, first strand: chain '2' and resid 380 through 382 removed outlier: 3.623A pdb=" N ILE 2 425 " --> pdb=" O ILE 2 402 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE 2 402 " --> pdb=" O ILE 2 425 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '2' and resid 397 through 399 Processing sheet with id= AB, first strand: chain '2' and resid 504 through 507 removed outlier: 5.987A pdb=" N VAL 2 644 " --> pdb=" O LEU 2 505 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS 2 507 " --> pdb=" O VAL 2 644 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS 2 646 " --> pdb=" O CYS 2 507 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB 724 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.98 Time building geometry restraints manager: 17.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6662 1.31 - 1.44: 9992 1.44 - 1.57: 22634 1.57 - 1.70: 120 1.70 - 1.83: 336 Bond restraints: 39744 Sorted by residual: bond pdb=" C THR 7 254 " pdb=" N ILE 7 255 " ideal model delta sigma weight residual 1.331 1.667 -0.336 1.32e-02 5.74e+03 6.50e+02 bond pdb=" C VAL 4 588 " pdb=" N LEU 4 589 " ideal model delta sigma weight residual 1.332 1.659 -0.326 1.40e-02 5.10e+03 5.44e+02 bond pdb=" C PHE 6 108 " pdb=" N THR 6 109 " ideal model delta sigma weight residual 1.328 1.523 -0.194 1.23e-02 6.61e+03 2.50e+02 bond pdb=" C PRO 7 267 " pdb=" N GLY 7 268 " ideal model delta sigma weight residual 1.331 1.536 -0.205 1.46e-02 4.69e+03 1.98e+02 bond pdb=" C THR 4 271 " pdb=" N ARG 4 272 " ideal model delta sigma weight residual 1.332 1.487 -0.155 1.29e-02 6.01e+03 1.44e+02 ... (remaining 39739 not shown) Histogram of bond angle deviations from ideal: 84.50 - 98.75: 32 98.75 - 113.01: 20863 113.01 - 127.27: 32412 127.27 - 141.53: 425 141.53 - 155.79: 5 Bond angle restraints: 53737 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 115.04 24.83 1.00e+00 1.00e+00 6.16e+02 angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 116.06 23.81 1.00e+00 1.00e+00 5.67e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 113.35 23.48 1.00e+00 1.00e+00 5.51e+02 angle pdb=" PB ATP 4 901 " pdb=" O3B ATP 4 901 " pdb=" PG ATP 4 901 " ideal model delta sigma weight residual 139.87 117.24 22.63 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP 6 901 " pdb=" O3B ATP 6 901 " pdb=" PG ATP 6 901 " ideal model delta sigma weight residual 139.87 118.05 21.82 1.00e+00 1.00e+00 4.76e+02 ... (remaining 53732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 23375 35.47 - 70.94: 862 70.94 - 106.41: 77 106.41 - 141.88: 7 141.88 - 177.36: 2 Dihedral angle restraints: 24323 sinusoidal: 10038 harmonic: 14285 Sorted by residual: dihedral pdb=" C PRO 5 419 " pdb=" N PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual -120.70 -153.65 32.95 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" CD ARG 6 427 " pdb=" NE ARG 6 427 " pdb=" CZ ARG 6 427 " pdb=" NH1 ARG 6 427 " ideal model delta sinusoidal sigma weight residual 0.00 119.81 -119.81 1 1.00e+01 1.00e-02 1.44e+02 dihedral pdb=" N PRO 5 419 " pdb=" C PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual 115.10 145.01 -29.91 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 24320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6043 0.584 - 1.168: 8 1.168 - 1.752: 17 1.752 - 2.336: 14 2.336 - 2.920: 1 Chirality restraints: 6083 Sorted by residual: chirality pdb=" CB VAL 4 652 " pdb=" CA VAL 4 652 " pdb=" CG1 VAL 4 652 " pdb=" CG2 VAL 4 652 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.13e+02 chirality pdb=" CB ILE 4 472 " pdb=" CA ILE 4 472 " pdb=" CG1 ILE 4 472 " pdb=" CG2 ILE 4 472 " both_signs ideal model delta sigma weight residual False 2.64 0.31 2.33 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" CB ILE 2 310 " pdb=" CA ILE 2 310 " pdb=" CG1 ILE 2 310 " pdb=" CG2 ILE 2 310 " both_signs ideal model delta sigma weight residual False 2.64 0.49 2.15 2.00e-01 2.50e+01 1.16e+02 ... (remaining 6080 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 510 " 0.443 9.50e-02 1.11e+02 2.26e-01 1.69e+02 pdb=" NE ARG 5 510 " -0.102 2.00e-02 2.50e+03 pdb=" CZ ARG 5 510 " 0.202 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 510 " -0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 510 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 641 " 0.459 9.50e-02 1.11e+02 2.29e-01 1.54e+02 pdb=" NE ARG 2 641 " -0.099 2.00e-02 2.50e+03 pdb=" CZ ARG 2 641 " 0.190 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 641 " -0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 641 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 629 " 0.070 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C ASP 7 629 " -0.211 2.00e-02 2.50e+03 pdb=" O ASP 7 629 " 0.067 2.00e-02 2.50e+03 pdb=" N VAL 7 630 " 0.075 2.00e-02 2.50e+03 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 4 1.80 - 2.58: 760 2.58 - 3.35: 53884 3.35 - 4.13: 93384 4.13 - 4.90: 156573 Nonbonded interactions: 304605 Sorted by model distance: nonbonded pdb=" NH2 ARG 7 219 " pdb=" CD ARG 6 263 " model vdw 1.031 3.520 nonbonded pdb=" NH2 ARG 7 219 " pdb=" CG ARG 6 263 " model vdw 1.233 3.520 nonbonded pdb=" OD2 ASP 3 397 " pdb=" CG1 VAL 7 246 " model vdw 1.371 3.460 nonbonded pdb=" O VAL 5 425 " pdb=" CG2 VAL 5 425 " model vdw 1.780 3.460 nonbonded pdb=" NZ LYS 5 384 " pdb=" OD1 ASN 5 486 " model vdw 1.918 2.520 ... (remaining 304600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 208 5.16 5 C 24484 2.51 5 N 6871 2.21 5 O 7479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.070 Check model and map are aligned: 0.590 Convert atoms to be neutral: 0.350 Process input model: 95.040 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.336 39744 Z= 0.836 Angle : 1.770 34.092 53737 Z= 1.007 Chirality : 0.162 2.920 6083 Planarity : 0.018 0.488 6914 Dihedral : 18.455 177.356 15020 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.77 % Allowed : 17.40 % Favored : 81.82 % Rotamer Outliers : 7.45 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.99 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.68 (0.09), residues: 4775 helix: -3.73 (0.09), residues: 1355 sheet: -3.86 (0.19), residues: 398 loop : -4.01 (0.09), residues: 3022 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1127 time to evaluate : 4.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 314 outliers final: 90 residues processed: 1354 average time/residue: 0.5442 time to fit residues: 1164.9762 Evaluate side-chains 792 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 702 time to evaluate : 4.625 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 90 outliers final: 3 residues processed: 90 average time/residue: 0.3754 time to fit residues: 68.0372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 408 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 203 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 439 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 194 GLN 3 199 GLN ** 3 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 448 ASN 3 546 HIS 4 204 HIS 4 223 GLN 4 228 GLN 4 326 ASN 4 441 HIS 4 494 HIS ** 4 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 625 GLN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 67 GLN 6 181 ASN 6 198 GLN 6 364 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 513 GLN 6 550 ASN 5 456 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 290 HIS A 296 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN N 69 GLN N 142 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN 2 227 HIS 2 352 GLN 2 364 GLN 2 450 GLN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 668 HIS 2 758 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 39744 Z= 0.268 Angle : 0.889 11.674 53737 Z= 0.460 Chirality : 0.051 0.243 6083 Planarity : 0.007 0.083 6914 Dihedral : 11.615 177.086 5481 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.98 % Favored : 86.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.60 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.10), residues: 4775 helix: -3.01 (0.11), residues: 1431 sheet: -3.36 (0.21), residues: 396 loop : -3.52 (0.10), residues: 2948 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 935 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 956 average time/residue: 0.5212 time to fit residues: 797.6279 Evaluate side-chains 677 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 672 time to evaluate : 4.671 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.3186 time to fit residues: 9.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 244 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 365 optimal weight: 0.0270 chunk 299 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 440 optimal weight: 0.9980 chunk 475 optimal weight: 1.9990 chunk 392 optimal weight: 0.0000 chunk 436 optimal weight: 2.9990 chunk 150 optimal weight: 0.3980 chunk 353 optimal weight: 0.8980 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 381 GLN ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 193 GLN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 217 HIS 4 475 ASN ** 4 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 595 GLN 4 656 GLN 7 45 GLN 7 69 ASN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 536 HIS ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 285 ASN 6 296 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 486 ASN 6 533 ASN 6 584 HIS 6 645 ASN 5 60 ASN ** 5 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 5 537 HIS A 182 GLN A 229 ASN A 264 HIS A 421 HIS A 431 GLN H 36 GLN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS M 131 HIS M 164 ASN N 162 ASN N 164 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 39744 Z= 0.201 Angle : 0.769 11.793 53737 Z= 0.394 Chirality : 0.047 0.320 6083 Planarity : 0.006 0.103 6914 Dihedral : 10.851 177.937 5481 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.96 % Favored : 86.95 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.10), residues: 4775 helix: -2.50 (0.12), residues: 1402 sheet: -2.81 (0.21), residues: 444 loop : -3.22 (0.10), residues: 2929 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 885 time to evaluate : 4.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 889 average time/residue: 0.5271 time to fit residues: 747.1062 Evaluate side-chains 648 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 643 time to evaluate : 4.837 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.3288 time to fit residues: 9.7966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 435 optimal weight: 0.1980 chunk 331 optimal weight: 0.0970 chunk 228 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 295 optimal weight: 0.0470 chunk 441 optimal weight: 1.9990 chunk 467 optimal weight: 0.9980 chunk 230 optimal weight: 4.9990 chunk 418 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 217 HIS ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 270 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS 6 486 ASN ** 6 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS 5 563 HIS A 264 HIS H 36 GLN ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS L 154 HIS M 151 ASN M 164 ASN N 110 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 39744 Z= 0.190 Angle : 0.722 10.928 53737 Z= 0.369 Chirality : 0.046 0.207 6083 Planarity : 0.005 0.062 6914 Dihedral : 10.358 179.488 5481 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.42 % Favored : 87.54 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.11), residues: 4775 helix: -2.20 (0.12), residues: 1386 sheet: -3.00 (0.20), residues: 520 loop : -2.95 (0.11), residues: 2869 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 836 time to evaluate : 5.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 838 average time/residue: 0.5275 time to fit residues: 714.7242 Evaluate side-chains 625 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 623 time to evaluate : 5.037 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3287 time to fit residues: 8.2921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 389 optimal weight: 0.0980 chunk 265 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 348 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 399 optimal weight: 4.9990 chunk 323 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 238 optimal weight: 0.5980 chunk 419 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 193 GLN ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 345 ASN ** 4 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 270 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 86 GLN 6 90 ASN 6 176 ASN ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 548 HIS A 264 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN M 166 GLN N 69 GLN ** N 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN 2 548 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5875 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 39744 Z= 0.170 Angle : 0.700 11.427 53737 Z= 0.354 Chirality : 0.045 0.239 6083 Planarity : 0.005 0.087 6914 Dihedral : 10.026 179.695 5481 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.29 % Favored : 88.69 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.11), residues: 4775 helix: -1.99 (0.13), residues: 1376 sheet: -2.77 (0.21), residues: 503 loop : -2.83 (0.11), residues: 2896 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 806 time to evaluate : 4.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 811 average time/residue: 0.5304 time to fit residues: 700.9639 Evaluate side-chains 613 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 611 time to evaluate : 4.843 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3331 time to fit residues: 8.0476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 157 optimal weight: 8.9990 chunk 421 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 274 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 468 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 216 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 0.2980 chunk 245 optimal weight: 1.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 378 HIS ** 4 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 90 ASN 6 231 GLN ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 563 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN M 164 ASN N 180 HIS ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 39744 Z= 0.164 Angle : 0.677 11.261 53737 Z= 0.343 Chirality : 0.044 0.202 6083 Planarity : 0.005 0.068 6914 Dihedral : 9.771 179.908 5481 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.60 % Favored : 88.38 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.11), residues: 4775 helix: -1.86 (0.13), residues: 1387 sheet: -2.59 (0.22), residues: 475 loop : -2.77 (0.11), residues: 2913 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 800 time to evaluate : 4.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 803 average time/residue: 0.5038 time to fit residues: 657.5348 Evaluate side-chains 618 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 616 time to evaluate : 4.477 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3133 time to fit residues: 7.7386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 451 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 394 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 466 optimal weight: 0.0770 chunk 291 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 215 optimal weight: 0.0970 overall best weight: 0.6336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 389 GLN 7 479 ASN 7 605 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 499 ASN 6 548 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 264 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN 2 450 GLN 2 516 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.305 39744 Z= 0.217 Angle : 0.692 17.266 53737 Z= 0.350 Chirality : 0.044 0.196 6083 Planarity : 0.005 0.075 6914 Dihedral : 9.611 179.898 5481 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.99 % Favored : 88.98 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.11), residues: 4775 helix: -1.71 (0.13), residues: 1409 sheet: -2.49 (0.23), residues: 456 loop : -2.72 (0.11), residues: 2910 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 785 time to evaluate : 5.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 790 average time/residue: 0.5248 time to fit residues: 679.5747 Evaluate side-chains 617 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 614 time to evaluate : 4.739 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.3607 time to fit residues: 8.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 288 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 90 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 337 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 371 HIS 4 507 HIS 7 238 GLN ** 7 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 563 HIS ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 290 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 39744 Z= 0.282 Angle : 0.802 12.410 53737 Z= 0.410 Chirality : 0.048 0.236 6083 Planarity : 0.006 0.064 6914 Dihedral : 9.842 178.475 5481 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 22.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.65 % Favored : 86.32 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.11), residues: 4775 helix: -1.90 (0.13), residues: 1429 sheet: -2.37 (0.23), residues: 425 loop : -2.74 (0.11), residues: 2921 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 792 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 794 average time/residue: 0.5371 time to fit residues: 692.2979 Evaluate side-chains 628 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 626 time to evaluate : 4.761 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3291 time to fit residues: 7.7853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 424 optimal weight: 0.3980 chunk 446 optimal weight: 4.9990 chunk 407 optimal weight: 0.6980 chunk 434 optimal weight: 4.9990 chunk 261 optimal weight: 0.1980 chunk 189 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 392 optimal weight: 0.4980 chunk 411 optimal weight: 0.9980 chunk 433 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 570 ASN ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 548 HIS ** 5 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS M 164 ASN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 39744 Z= 0.185 Angle : 0.722 13.209 53737 Z= 0.363 Chirality : 0.045 0.214 6083 Planarity : 0.005 0.068 6914 Dihedral : 9.598 178.339 5481 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.52 % Favored : 88.46 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.11), residues: 4775 helix: -1.76 (0.13), residues: 1436 sheet: -2.46 (0.23), residues: 430 loop : -2.70 (0.11), residues: 2909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 797 time to evaluate : 4.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 799 average time/residue: 0.5287 time to fit residues: 684.1662 Evaluate side-chains 607 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 605 time to evaluate : 4.750 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3217 time to fit residues: 7.8941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 285 optimal weight: 0.0030 chunk 459 optimal weight: 2.9990 chunk 280 optimal weight: 0.0870 chunk 218 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 482 optimal weight: 0.0370 chunk 443 optimal weight: 0.4980 chunk 383 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 296 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.2246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 245 ASN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 181 ASN ** 6 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 563 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 467 HIS L 51 HIS M 164 ASN ** N 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.7587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.180 39744 Z= 0.503 Angle : 0.756 50.466 53737 Z= 0.391 Chirality : 0.045 0.220 6083 Planarity : 0.005 0.101 6914 Dihedral : 9.378 176.712 5481 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.71 % Favored : 88.27 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.11), residues: 4775 helix: -1.62 (0.13), residues: 1431 sheet: -2.40 (0.22), residues: 465 loop : -2.68 (0.11), residues: 2879 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 777 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 779 average time/residue: 0.5185 time to fit residues: 657.9912 Evaluate side-chains 610 residues out of total 4296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 608 time to evaluate : 4.714 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.3282 time to fit residues: 7.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 304 optimal weight: 0.2980 chunk 409 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 354 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 384 optimal weight: 0.5980 chunk 160 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 467 GLN ** 3 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 223 GLN ** 4 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 371 HIS ** 7 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 439 GLN ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 605 ASN ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 HIS ** 6 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 548 HIS ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 467 HIS L 51 HIS M 53 ASN M 164 ASN ** N 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 239 GLN ** 2 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN ** 2 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.221335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.205428 restraints weight = 118196.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.206314 restraints weight = 97664.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.207079 restraints weight = 84952.489| |-----------------------------------------------------------------------------| r_work (final): 0.4634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.7769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.714 39744 Z= 0.350 Angle : 0.734 39.036 53737 Z= 0.377 Chirality : 0.044 0.207 6083 Planarity : 0.005 0.106 6914 Dihedral : 9.334 178.613 5481 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.31 % Favored : 88.63 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 4775 helix: -1.58 (0.13), residues: 1443 sheet: -2.35 (0.23), residues: 454 loop : -2.65 (0.11), residues: 2878 =============================================================================== Job complete usr+sys time: 11269.44 seconds wall clock time: 202 minutes 56.67 seconds (12176.67 seconds total)